An immunoinformatics and extensive molecular dynamics study to develop a polyvalent multi-epitope vaccine against cryptococcosis

Md. Razwan Sardar Sami; Nurul Amin Rani; Mohammad Mahfuz Enam Elahi; Mohammad Sajjad Hossain; Minhaz Abdullah Al Mueid; Zahidur Rahim; Rajesh B. Patil; Abu Tayab Moin; Israt Jahan Bithi; Sabekun Nahar; Israt Jahan Konika; Sneha Roy; Jannatul Aleya Preya; Jamil Ahmed

doi:10.1371/journal.pone.0315105

Peer Review History

Original SubmissionAugust 14, 2024
21 Aug 2024 Decision Letter - Sheikh Arslan Sehgal, Editor PONE-D-24-29190An Immunoinformatics and Extensive Molecular Dynamics Study to Develop a Polyvalent Multi-Epitope Vaccine Against CryptococcosisPLOS ONE Dear Dr. Ahmed, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Oct 05 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: N/A ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: This study provided sufficient experimental evidence to support the conclusion. Overall, the results are solid and consistent. Several issues still need to be addressed before publication. The following questions may help the authors to improve the quality of their already outstanding manuscript, e.g. some important references are missing, such as PMID: 17038537; PMID: 20889547; PMID: 18490721;PMID: 38700327；PMID: 38075876 ； PMID: 37245745； PMID: 36094198 ；PMID: 35720422 Reviewer #2: Thank you for submitting your manuscript. After a thorough evaluation, I would like to provide some critical feedback to help improve the quality and clarity of your work. Please consider the following points in your revisions: 1. Docking Protocol Validation: Please provide a detailed explanation of how you validated the docking protocol used in your study. Consider discussing any re-docking procedures or comparisons with known complexes that were performed to ensure the reliability of your docking results. 2. Rationale for 100 ns Simulation: Clarify the rationale behind choosing 100 ns for your molecular dynamics (MD) simulations. Explain why this duration was deemed sufficient for observing the stability and dynamics of the protein-ligand complex relevant to the vaccine. If possible, consider extending the simulation to provide more robust data on the system's behavior over time. 3. Laboratory Assay Validation: While computational predictions are valuable, please acknowledge that laboratory assays are essential for validating the efficacy of your proposed vaccine. Discuss the limitations of your study due to the absence of experimental validation and suggest potential future experiments that could confirm your computational findings. 4. Methodology Clarification: Justify your choice of methods, software, and parameters used throughout the study. Ensure that all selected approaches are well-explained, and provide additional details on the parameters used in docking and MD simulations. 5. Discussion Section Enhancement: Strengthen the discussion by linking your computational results more explicitly to their biological significance. Compare your findings with existing vaccines or known immunogenic epitopes, and suggest directions for future research that could build on your results. 6. Comprehensive Results Analysis: Ensure that all significant data, such as binding energies and structural changes, are thoroughly analyzed and presented. Consider adding more visuals, such as graphs, figures, and tables, to enhance the readability and impact of your results. 7. Graphical Illustration of Interacting Residues: I suggest providing a more detailed graphical illustration of interacting residues between the protein and ligand molecule (which can be derived from the PDBsum server) in the results section. This would add clarity to your findings and support your conclusions. 8. Correction of Grammatical Errors: Review the manuscript for grammatical errors and inconsistencies. Ensuring that the language is clear and free of errors will improve the overall readability and professionalism of your manuscript. 9. Writing and Structural Improvements: Review the manuscript for clarity and consistency. Simplify the writing where possible, and ensure that terminology is used consistently throughout the manuscript to avoid confusion. These suggestions aim to improve the overall rigor, clarity, and impact of your manuscript. I believe addressing these points will significantly enhance the quality of your work. Thank you for your attention to these matters. I look forward to seeing the revised version of your manuscript. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0315105.r001
Revision 1
14 Nov 2024 Author Response Reponses to the Reviewers Reviewer #1: This study provided sufficient experimental evidence to support the conclusion. Overall, the results are solid and consistent. Several issues still need to be addressed before publication. The following questions may help the authors to improve the quality of their already outstanding manuscript, e.g. some important references are missing, such as PMID: 17038537; PMID: 20889547; PMID: 18490721; PMID: 38700327；PMID: 38075876 ； PMID: 37245745； PMID: 36094198 ；PMID: 35720422 Reply: Thank you for your kind recognition. We have included all this references to robust the quality of our manuscript. Thank you. Reviewer #2: Thank you for submitting your manuscript. After a thorough evaluation, I would like to provide some critical feedback to help improve the quality and clarity of your work. Please consider the following points in your revisions: 1. Docking Protocol Validation: Please provide a detailed explanation of how you validated the docking protocol used in your study. Consider discussing any re-docking procedures or comparisons with known complexes that were performed to ensure the reliability of your docking results. Reply: Thank you for the valuable comment. We have used docking protocol that is established for Vaccine-TLR complex using Cluspro and HDOCK server. ClusPro and HDOCK are well-established docking tools, frequently cited in the literature for their accuracy in protein-protein and protein-ligand docking. The Cluspro server characterizes docked models by the centers of densely packed clusters of low-energy docked structures. It is also mentioned in the manuscript. Additionally, we have compared the result of previous complex of same TLRs with our designed complex. Which is described in detail in the discussion portion. Thank you. References: Amin Rani N, Moin AT, Patil R, Barketullah Robin T, Zubair T, Nawal N, et al. Designing a polyvalent vaccine targeting multiple strains of varicella zoster virus using integrated bioinformatics approaches. Frontiers in Microbiology. 2023;14:1291868. DOI: 10.3389/fmicb.2023.1291868 Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, et al. The ClusPro web server for protein–protein docking. Nature protocols. 2017;12(2):255-78. 2. Rationale for 100 ns Simulation: Clarify the rationale behind choosing 100 ns for your molecular dynamics (MD) simulations. Explain why this duration was deemed sufficient for observing the stability and dynamics of the protein-ligand complex relevant to the vaccine. If possible, consider extending the simulation to provide more robust data on the system's behavior over time. Reply: Dear Reviewer, thank you for your insightful comment on the rationale for selecting a 100 ns duration for our molecular dynamics (MD) simulations. We are pleased to provide further clarification on this choice and its relevance to our study. The 100 ns timeframe is widely adopted in MD simulations to achieve an in-depth examination of protein-ligand interactions, including stability, flexibility, and binding dynamics, particularly in systems like the TLR-vaccine complexes in our research. Extensive studies demonstrate that this duration allows for robust observation of equilibrium states and dynamic behavior, especially in systems where structural stability and binding consistency are primary indicators. For instance, research by Shaw et al. (2010) and Hollingsworth et al. (2018) highlights that 100 ns simulations are generally effective in capturing key conformational stability metrics, such as Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF), which help verify that the system has achieved a stable conformation indicative of natural binding behavior. In our study, after conducting preliminary analyses on RMSD, RMSF, and hydrogen bonding stability over the 100 ns span, we observed that each system reached a stable conformation. These indicators not only demonstrate stability but are also sufficient to interpret the relevant interactions of TLRs with vaccine constructs, confirming the reliability of observed trends within this timeframe. Additionally, energy convergence and solvent accessibility analysis further support that the 100 ns simulation provides the necessary data for understanding the protein-ligand interactions at a meaningful resolution. By ensuring that the simulation time is sufficiently long to capture the equilibrium states and primary dynamic interactions, we aim to provide accurate and reliable insights into the stability and binding properties of the TLR-vaccine complexes. We hope this expanded explanation addresses your concern. Thank you once again for the opportunity to clarify our approach. References: Shaw DE, Maragakis P, Lindorff-Larsen K, et al. Atomic-Level Characterization of the Structural Dynamics of Proteins. Science. 2010;330(6002):341-346. doi:10.1126/science.1187409. Hollingsworth SA, Dror RO. Molecular Dynamics Simulation for All. Neuron. 2018;99(6):1129-1143. doi:10.1016/j.neuron.2018.08.011 3. Laboratory Assay Validation: While computational predictions are valuable, please acknowledge that laboratory assays are essential for validating the efficacy of your proposed vaccine. Discuss the limitations of your study due to the absence of experimental validation and suggest potential future experiments that could confirm your computational findings. Reply: Thank you for the valuable comment. We have added the acknowledgement of the need for laboratory validation and also discuss the limitation of our study along with probable future experimental direction. You can find this information in the last portion of discussion section. Thank you again. 4. Methodology Clarification: Justify your choice of methods, software, and parameters used throughout the study. Ensure that all selected approaches are well-explained, and provide additional details on the parameters used in docking and MD simulations. Reply: Thank you. We have added detailed explanation of the tools and approaches being used during the study. Additionally, supplementary table S6 represents specific application and description of different tools used in this research. The detail information on the parameters used in docking and MD simulations was also discussed in the manuscript. Thank you. 5. Discussion Section Enhancement: Strengthen the discussion by linking your computational results more explicitly to their biological significance. Compare your findings with existing vaccines or known immunogenic epitopes, and suggest directions for future research that could build on your results. Reply: Thank you. We have analysed the findings in a detail manner and also compared our findings with existing vaccines against fungal pathogen. Thank you. 6. Comprehensive Results Analysis: Ensure that all significant data, such as binding energies and structural changes, are thoroughly analyzed and presented. Consider adding more visuals, such as graphs, figures, and tables, to enhance the readability and impact of your results. Reply: Thank you for the valuable comment. We have included a figure that represents the best docked complex with their binding energy (Figure 2). Also added a table in the manuscript that contains all the necessary information regarding the properties of the constructed vaccines (Table 2). Additionally, we have presented further detailing through figures and tables in our supplementary file in a very organized manner to enhance the readability and understanding. Thank you again. 7. Graphical Illustration of Interacting Residues: I suggest providing a more detailed graphical illustration of interacting residues between the protein and ligand molecule (which can be derived from the PDBsum server) in the results section. This would add clarity to your findings and support your conclusions. Reply: Thank you for your valuable comment. The detailed graphical illustration of interacting residues between the protein and ligand molecule is added as a figure in the supplementary figure S6 and the relevant information is added in the manuscript. We have employed the Pymol software for generating the interacting residue. We could not use PDBsum server because the server is not working smoothly in our country, but we have used a different software to generate interacting residue in the form of amino acid. Thank you again. 8. Correction of Grammatical Errors: Review the manuscript for grammatical errors and inconsistencies. Ensuring that the language is clear and free of errors will improve the overall readability and professionalism of your manuscript. Reply: Thank you for your comment. We have reviewed the whole manuscript and corrected all the grammatical errors and inconsistency. Thank you 9. Writing and Structural Improvements: Review the manuscript for clarity and consistency. Simplify the writing where possible, and ensure that terminology is used consistently throughout the manuscript to avoid confusion. Reply: Thank you for the comment. We have thoroughly checked the writing and improved the overall quality. We have also improved consistency of our manuscript. Thank you. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0315105.r002
21 Nov 2024 Decision Letter - Sheikh Arslan Sehgal, Editor An Immunoinformatics and Extensive Molecular Dynamics Study to Develop a Polyvalent Multi-Epitope Vaccine Against Cryptococcosis PONE-D-24-29190R1 Dear Dr. Ahmed, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. 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If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: This is a revision; they have addressed all my concerns, and now it is acceptable. This is a revision; they have addressed all my concerns, and now it is acceptable. This is a revision; they have addressed all my concerns, and now it is acceptable. Reviewer #2: (No Response) ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No ******** https://doi.org/10.1371/journal.pone.0315105.r003
Formally Accepted
18 Dec 2024 Acceptance Letter - Sheikh Arslan Sehgal, Editor PONE-D-24-29190R1 PLOS ONE Dear Dr. Ahmed, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr Sheikh Arslan Sehgal Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0315105.r004

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